Summary

Target folder: C:/Git/ETN_workshop_Jan2021/actel_example

Timestamp: 2021-01-25 15:38:14

Number of target tags: 60

Number of listed receivers: 17 (of which 1 had no detections)

Data time range: 2018-04-13 22:26:37 to 2018-05-25 17:46:13 (Europe/Copenhagen).

Percentage of post-release valid detections: 100%

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Study area

Arrays with the same background belong to the same section. Release sites are marked with “R.S.”. Arrays connected with an arrow indicate that the animals can only pass in one direction.

Receiver stations

Station.name Latitude Longitude x y Array Section Standard.name
Station -1 56.35474 8.629019 477075.2 6245625 A0 River St.1
Station 1 56.35672 8.603097 475474.6 6245854 A1 River St.2
Station 2 56.36505 8.510094 469734.4 6246818 A2 River St.3
Station 3 56.34976 8.385683 462033.4 6245178 A3 River St.4
Station 4 56.32894 8.309133 457279.2 6242906 A4 River St.5
Station 5 56.32576 8.306444 457109.4 6242553 A5 River St.6
Station 6 56.32267 8.303267 456909.4 6242211 A6 River St.7
Station 7 56.32865 8.249125 453568.3 6242912 A7 Fjord St.8
Station 8 56.32610 8.246447 453399.6 6242630 A7 Fjord St.9
Station 9 56.32388 8.240797 453047.5 6242387 A7 Fjord St.10
Station 10 56.32192 8.239672 452975.5 6242169 A7 Fjord St.11
Station 11 56.37173 8.132342 446407.4 6247792 A8 Fjord St.12
Station 12 56.37221 8.130017 446264.5 6247847 A8 Fjord St.13
Station 13 56.37250 8.127761 446125.6 6247881 A8 Fjord St.14
Station 14 56.37199 8.118439 445549.1 6247831 A9 Sea St.15
Station 15 56.37256 8.118169 445533.2 6247895 A9 Sea St.16
Station 16 56.37200 8.117658 445500.9 6247833 A9 Sea St.17

Deployments

Receiver Array Station.name Standard.name Start Stop
132907 A0 Station -1 St.1 2018-03-15 12:00:00 2018-06-01 12:00:00
132908 A1 Station 1 St.2 2018-03-15 12:00:00 2018-06-01 12:00:00
132909 A7 Station 7 St.8 2018-03-15 12:00:00 2018-06-01 12:00:00
132914 A5 Station 5 St.6 2018-03-15 12:00:00 2018-06-01 12:00:00
132915 A6 Station 6 St.7 2018-03-15 12:00:00 2018-06-01 12:00:00
132916 A4 Station 4 St.5 2018-03-15 12:00:00 2018-06-01 12:00:00
132917 A3 Station 3 St.4 2018-03-15 12:00:00 2018-06-01 12:00:00
132918 A2 Station 2 St.3 2018-03-15 12:00:00 2018-06-01 12:00:00
133205 A8 Station 13 St.14 2018-03-15 12:00:00 2018-06-01 12:00:00
133206 A9 Station 16 St.17 2018-03-15 12:00:00 2018-06-01 12:00:00
133209 A8 Station 12 St.13 2018-03-15 12:00:00 2018-06-01 12:00:00
133210 A9 Station 14 St.15 2018-03-15 12:00:00 2018-06-01 12:00:00
133215 A9 Station 15 St.16 2018-03-15 12:00:00 2018-06-01 12:00:00
133220 A8 Station 11 St.12 2018-03-15 12:00:00 2018-06-01 12:00:00
133221 A7 Station 10 St.11 2018-03-15 12:00:00 2018-06-01 12:00:00
133222 A7 Station 8 St.9 2018-03-15 12:00:00 2018-06-01 12:00:00
133224 A7 Station 9 St.10 2018-03-15 12:00:00 2018-06-01 12:00:00

Release sites

Station.name Latitude Longitude x y Array Type Standard.name n.A n.B
RS1 56.349 8.6204 476539 6244988 A1 Release RS1 30 30

Array efficiency

Note:
More information on the differences between “Known missed events” and “Potentially missed events” can be found in the package vignettes.
The data used in this table is stored in the efficiency object.
These efficiency values are estimated using a simple step-by-step method (described in the package vignettes). In some situations, more advanced efficiency estimation methods may be required.
You can try running advEfficiency(results$efficiency) to obtain beta-drawn efficiency distributions (replace results with the name of the object where you saved the analysis).

Events recorded and missed

A0 A1 A2 A3 A4 A5 A6 A7 A8 A9
Recorded events 0 54 54 52 54 54 52 49 46 37
Known missed events - 0 0 2 0 0 0 1 0 -
Potentially missed events - 0 0 0 0 0 0 0 0 -

Array efficiency

Note: These values already include any intra-array efficiency estimates that have been requested.

A0 A1 A2 A3 A4 A5 A6 A7 A8 A9
Maximum efficiency - 100% 100% 96.3% 100% 100% 100% 98% 100% -
Minimum efficiency - 100% 100% 96.3% 100% 100% 100% 98% 100% -

Warning messages

Warning: GUI is set to 'needed' but packages 'gWidgets2', 'gWidgets2RGtk2', 'RGtk2' are not available. Please install them if you intend to run GUI.
         Disabling GUI (i.e. GUI = 'never') for the current run.
Warning: No detections were found for receiver(s) 132907.
Warning: 'speed.warning'/'speed.error' were not set, skipping speed checks.
Warning: 'inactive.warning'/'inactive.error' were not set, skipping inactivity checks.
Warning: Section movements with less than 2 detections are present for tag R64K-4503 (28/54).

User comments

R64K-4503   This is a lovely fish

Biometric graphics

Note:
The data used in this graphic is the data present in the biometrics.csv file.

Last seen

Note:
The data used in this table and graphic is stored in the last.seen object.
Disap. in River Disap. in Fjord Disap. in Sea Disap. at Release
A 0 6 20 4
B 4 9 15 2

Average time of arrival at each Array

Note:
Coloured lines on the outer circle indicate the mean value for each group and the respective ranges show the standard error of the mean. Each group’s bars sum to 100%. The number of data points in each group is presented between brackets in the legend of each pannel.
You can replicate these graphics and edit them as needed using the plotTimes() function.
The data used in these graphics is stored in the array.times object.
C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png

Time details for each section

Arrival days at each section

Note:
The data used in these graphics is stored in the section.times$arrival object.

Arrival times at each section

Note:
Coloured lines on the outer circle indicate the mean value for each group and the respective ranges show the standard error of the mean. Each group’s bars sum to 100%. The number of data points in each group is presented between brackets in the legend of each pannel.
You can replicate these graphics and edit them as needed using the plotTimes() function.
The data used in these graphics is stored in the section.times$arrival object.
C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png

Departure days at each section

Note:
The data used in these graphics is stored in the section.times$departure object.

Departure times at each section

Note:
Coloured lines on the outer circle indicate the mean value for each group and the respective ranges show the standard error of the mean. Each group’s bars sum to 100%. The number of data points in each group is presented between brackets in the legend of each pannel.
You can replicate these graphics and edit them as needed using the plotTimes() function.
The data used in these graphics is stored in the section.times$departure object.
C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png

Global residency

Note:
The data used in these graphics is stored in the global.ratios and time.positions objects.
You can replicate these graphics and edit them as needed using the plotRatios() function.
This data is also available split by group in the group.ratiosobject.
You can plot these results by group using the ‘group’ argument in plotRatios().

Absolutes

Percentages

Individual residency plots

Note:
The data used in these graphics is stored in the time.ratios object (one table per tag). More condensed information can be found in the section.movements object.
You can replicate these graphics and edit them as needed using the plotResidency() function.

Individual detection plots

Note:
You can choose to plot detections by station or by array using the detections.y.axis argument.
The detections are coloured by section. The vertical black dashed line shows the release time. The full dark-grey line shows the movement events considered valid, while the dashed dark-grey line shows the movement events considered invalid.
Manually edited tags are highlighted with yellow graphic borders.
Manually overridden tags are highlighted with red graphic borders.
The arrays have been aligned by section, following the order provided either in the spatial input or the section.order argument.
You can replicate these graphics and edit them as needed using the plotDetections() function.
You can also see the movement events of multiple tags simultaneously using the plotMoves() function.
The data used in these graphics is stored in the detections and movements objects (and respective valid counterparts).

Sensor plots

Note:
The colouring in these plots will follow that of the individual detection plots, which can be modified using detections.y.axis.
The data used for these graphics is stored in the valid.detections object.
You can replicate these graphics and edit them as needed using the plotSensors() function.

Full log

Actel R package report.
Version: 1.2.1

Target folder: C:/Git/ETN_workshop_Jan2021/actel_example
Timestamp: 2021-01-25 15:38:14
Function: residency()

M: 'report' option has been activated.
M: Importing data. This process may take a while.
M: Number of target tags: 60.
M: Matching detections with deployment periods.
M: Number of ALS: 17 (of which 1 had no detections)
Warning: No detections were found for receiver(s) 132907.
M: Data time range: 2018-04-13 22:26:37 to 2018-05-25 17:46:13 (Europe/Copenhagen).
M: File 'distances.csv' found, activating speed calculations.
M: Data successfully imported!
M: Creating movement records for the valid tags.
M: Checking movement events quality.
Warning: 'speed.warning'/'speed.error' were not set, skipping speed checks.
Warning: 'inactive.warning'/'inactive.error' were not set, skipping inactivity checks.
M: Compiling and checking section movements for the valid tags.
Warning: Section movements with less than 2 detections are present for tag R64K-4503 (28/54).
M: Filtering valid array movements.
M: Filtering valid section movements.
M: Compiling residency objects.
M: Calculating daily locations for each tag.
M: Calculating inter-array efficiency.
M: Saving results as 'actel_residency_results.RData'.
M: Producing the report.
M: Drawing individual detection graphics.
M: Drawing individual residency graphics.
M: Printing sensor values for tags with sensor data.
M: Process finished successfully.

-------------------
User comments:
-------------------
R64K-4503: This is a lovely fish
-------------------
User interventions:
-------------------
comment # on R64K-4503
This is a lovely fish
n # invalidate/expand moves in R64K-4503?
y # save results?
-------------------
Function call:
-------------------
residency(tz = 'Europe/Copenhagen', section.order = NULL, datapack = NULL, max.interval = 60, minimum.detections = 2, start.time = NULL, stop.time = NULL, speed.method = c('last to first'), speed.warning = NULL, speed.error = NULL, jump.warning = 2, jump.error = 3, inactive.warning = NULL, exclude.tags = NULL, override = NULL, report = TRUE, auto.open = TRUE, discard.orphans = FALSE, discard.first = NULL, save.detections = FALSE, section.minimum = 2, timestep = 'days', replicates = NULL, inactive.error = NULL, GUI = 'never', save.tables.locally = FALSE, print.releases = TRUE, detections.y.axis = 'auto')
-------------------

Index:

Summary Study area Stations Deployments Release sites Array efficiency Warnings Comments Biometrics Last seen Array times Section times Global residency Individual residency Individual detections Sensor data Full log